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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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T2D-268 Report missing chromosome if fail to download from ENA #182

Closed Zhicheng-Liu closed 5 years ago

Zhicheng-Liu commented 5 years ago

This is to fix an issue when fail to download from ENA, the assembly checker continues to check the reference sequences and report mismatches:

If a contig is not found in ENA, an empty sequence is stored, but it silently fails to check the allele, saying: Line 5: Chromosome 1, position 500, reference allele 'C' does not match the reference sequence, expected ''

jmmut commented 5 years ago

Also, not strictly the same problem of this ticket, but if a position in the VCF is greater than the sequence length in the fasta, the same message of this ticket appears:

Line 3: Chromosome II, position 2000, reference allele 'A' does not match the reference sequence, expected ''

unlike in the bug that this PR solves, this time it's always correct that it's a mismatch, but the message is misleading in my opinion.